Package picard.analysis

Class CollectQualityYieldMetricsSNVQ.QualityYieldMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetricsSNVQ.QualityYieldMetrics
Enclosing class:
CollectQualityYieldMetricsSNVQ
@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class CollectQualityYieldMetricsSNVQ.QualityYieldMetrics extends MergeableMetricBase
A set of metrics used to describe the general quality of a BAM file

  • Nested Class Summary

    Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase

    MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected final String
    alternateQualityAttribute
     
    double
    PCT_PF_Q20_BASES
    The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter
    double
    PCT_PF_Q20_SNVQ
    The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter
    double
    PCT_PF_Q30_BASES
    The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter
    double
    PCT_PF_Q30_SNVQ
    The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter
    double
    PCT_PF_Q40_BASES
    The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter
    double
    PCT_PF_Q40_SNVQ
    The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter
    double
    PCT_Q20_BASES
    The percentage of SNVQ values in all reads that achieve quality score 20 or higher
    double
    PCT_Q20_SNVQ
    The percentage of SNVQ values in all reads that achieve quality score 20 or higher
    double
    PCT_Q30_BASES
    The percentage of SNVQ values in all reads that achieve quality score 30 or higher
    double
    PCT_Q30_SNVQ
    The percentage of SNVQ values in all reads that achieve quality score 30 or higher
    double
    PCT_Q40_BASES
    The percentage of SNVQ values in all reads that achieve quality score 40 or higher
    double
    PCT_Q40_SNVQ
    The percentage of SNVQ values in all reads that achieve quality score 40 or higher
    long
    PF_BASES
    The total number of bases in all PF reads
    long
    PF_Q20_BASES
    The number of bases in PF reads that achieve quality score 20 or higher
    long
    PF_Q20_SNVQ
    The number of SNVQ values in PF reads that achieve quality score 20 or higher
    long
    PF_Q30_BASES
    The number of bases in PF reads that achieve quality score 30 or higher
    long
    PF_Q30_SNVQ
    The number of SNVQ values in PF reads that achieve quality score 30 or higher
    long
    PF_Q40_BASES
    The number of bases in PF reads that achieve quality score 40 or higher
    long
    PF_Q40_SNVQ
    The number of SNVQ values in PF reads that achieve quality score 40 or higher
    long
    PF_READS
    The number of reads that are PF - pass filter
    long
    PF_SNVQ
    The total number of SNVQ values in all PF reads
    long
    Q20_BASES
    The number of bases in all reads that achieve quality score 20 or higher
    long
    Q20_SNVQ
    The number of SNVQ values in all reads that achieve quality score 20 or higher
    long
    Q30_BASES
    The number of bases in all reads that achieve quality score 30 or higher
    long
    Q30_SNVQ
    The number of SNVQ values in all reads that achieve quality score 30 or higher
    long
    Q40_BASES
    The number of bases in all reads that achieve quality score 40 or higher
    long
    Q40_SNVQ
    The number of SNVQ values in all reads that achieve quality score 40 or higher
    int
    READ_LENGTH
    The average read length of all the reads
    long
    TOTAL_BASES
    The total number of bases in all reads
    long
    TOTAL_READS
    The total number of reads in the input file
    long
    TOTAL_SNVQ
    The total number of SNVQ values in all reads

  • Constructor Summary

    Constructors
    Constructor
    Description
    QualityYieldMetrics()
     
    QualityYieldMetrics(String alternateQualityAttribute)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    calculateDerivedFields()
    Placeholder method that will calculate the derived fields from the other ones.
    MergeableMetricBase
    merge(MergeableMetricBase other)
    Merge another metric into this one

    Methods inherited from class picard.analysis.MergeableMetricBase

    canMerge, merge, mergeIfCan

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • TOTAL_READS

      public long TOTAL_READS
      The total number of reads in the input file

    • PF_READS

      public long PF_READS
      The number of reads that are PF - pass filter

    • READ_LENGTH

      public int READ_LENGTH
      The average read length of all the reads

    • TOTAL_BASES

      public long TOTAL_BASES
      The total number of bases in all reads

    • PF_BASES

      public long PF_BASES
      The total number of bases in all PF reads

    • Q20_BASES

      public long Q20_BASES
      The number of bases in all reads that achieve quality score 20 or higher

    • PF_Q20_BASES

      public long PF_Q20_BASES
      The number of bases in PF reads that achieve quality score 20 or higher

    • Q30_BASES

      public long Q30_BASES
      The number of bases in all reads that achieve quality score 30 or higher

    • PF_Q30_BASES

      public long PF_Q30_BASES
      The number of bases in PF reads that achieve quality score 30 or higher

    • Q40_BASES

      public long Q40_BASES
      The number of bases in all reads that achieve quality score 40 or higher

    • PF_Q40_BASES

      public long PF_Q40_BASES
      The number of bases in PF reads that achieve quality score 40 or higher

    • PCT_Q20_BASES

      public double PCT_Q20_BASES
      The percentage of SNVQ values in all reads that achieve quality score 20 or higher

    • PCT_Q30_BASES

      public double PCT_Q30_BASES
      The percentage of SNVQ values in all reads that achieve quality score 30 or higher

    • PCT_Q40_BASES

      public double PCT_Q40_BASES
      The percentage of SNVQ values in all reads that achieve quality score 40 or higher

    • PCT_PF_Q20_BASES

      public double PCT_PF_Q20_BASES
      The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter

    • PCT_PF_Q30_BASES

      public double PCT_PF_Q30_BASES
      The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter

    • PCT_PF_Q40_BASES

      public double PCT_PF_Q40_BASES
      The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter

    • TOTAL_SNVQ

      public long TOTAL_SNVQ
      The total number of SNVQ values in all reads

    • PF_SNVQ

      public long PF_SNVQ
      The total number of SNVQ values in all PF reads

    • Q20_SNVQ

      public long Q20_SNVQ
      The number of SNVQ values in all reads that achieve quality score 20 or higher

    • PF_Q20_SNVQ

      public long PF_Q20_SNVQ
      The number of SNVQ values in PF reads that achieve quality score 20 or higher

    • Q30_SNVQ

      public long Q30_SNVQ
      The number of SNVQ values in all reads that achieve quality score 30 or higher

    • PF_Q30_SNVQ

      public long PF_Q30_SNVQ
      The number of SNVQ values in PF reads that achieve quality score 30 or higher

    • Q40_SNVQ

      public long Q40_SNVQ
      The number of SNVQ values in all reads that achieve quality score 40 or higher

    • PF_Q40_SNVQ

      public long PF_Q40_SNVQ
      The number of SNVQ values in PF reads that achieve quality score 40 or higher

    • PCT_Q20_SNVQ

      public double PCT_Q20_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 20 or higher

    • PCT_Q30_SNVQ

      public double PCT_Q30_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 30 or higher

    • PCT_Q40_SNVQ

      public double PCT_Q40_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 40 or higher

    • PCT_PF_Q20_SNVQ

      public double PCT_PF_Q20_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter

    • PCT_PF_Q30_SNVQ

      public double PCT_PF_Q30_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter

    • PCT_PF_Q40_SNVQ

      public double PCT_PF_Q40_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter

    • alternateQualityAttribute

      protected final String alternateQualityAttribute

  • Constructor Details

    • QualityYieldMetrics

      public QualityYieldMetrics()

    • QualityYieldMetrics

      public QualityYieldMetrics(String alternateQualityAttribute)

  • Method Details